Cerberus isn't just an organization or the people behind it. Cerberus is an idea; that idea is not so easily destroyed.
Cerberus is a group from the Mass Effect series and a stable in EDBW. It is associated with, but not necessarily encompassing, the EDBW Trio of the same name, and the current known members are The Illusive Man and Commander Shepard.
The existence of Cerberus was first hinted at at the end of Killscreen IV, where Monokuma was seen talking to an offscreen ally of his, who would later be revealed as Commander Shepard. Monokuma would later initiate EDBW's Lockdown, presumably as part of their overall plan, before he was abandoned and remotely shut down by Cerberus after his defeat at Killscreen V.
After wiping Monokuma's memory of the organization, Commander Shepard would become Cerberus's primary agent in EDBW, assembling a team of allies (using the name Cerberus for that as well) and taking steps in secret to further Cerberus's plans within EDBW. At the end of EDBW: The Golden, Shepard was seen making some sort of offer to Lucas, and later on spoke to the Illusive Man about someone having an "unexpected reaction to implants", but otherwise Cerberus's greater goals are still in the shadows.